pull DP from VCF and show

R/input_data.R

@@ -152,7 +152,7 @@ load_germline_snv_indel <- function(
   if (as.logical(
     conf$variant_classification$secondary_findings) == TRUE) {
     if(as.logical(
-      conf$sample_properties$genotypes_available) == F){
+      conf$sample_properties$gt_detected) == F){
       pcgrr::log4r_warn(paste0(
         "Assessment of secondary variant findings (ACMG SF v3.2) ",
         "NOT possible - variant genotype information unavailable"

R/main.R

@@ -284,7 +284,7 @@ write_cpsr_output <- function(report,
     settings[["conf"]][["visual_reporting"]][["visual_theme"]]
 
   if (output_format == "html") {
-    if(report$content$snv_indel$v_stat_cpg$n < 2000){
+    if(report$content$snv_indel$v_stat_cpg$n < 3000){
       if(file.exists(quarto_input)){
 
         ## make temporary directory for quarto report rendering

data-raw/data-raw.R

@@ -10,6 +10,7 @@ col_format_output[['html_tier']] <-
     "GENOTYPE",
     "GENENAME",
     "PROTEIN_DOMAIN",
+    "DP_CONTROL",
     "HGVSp",
     "HGVSc",
     "ENSEMBL_GENE_ID",
@@ -55,6 +56,7 @@ col_format_output[['html_sf']] <-
     "GENOTYPE",
     "GENENAME",
     "PROTEIN_DOMAIN",
+    "DP_CONTROL",
     "HGVSp",
     "HGVSc",
     "ENSEMBL_GENE_ID",
@@ -87,6 +89,7 @@ col_format_output[['html_gwas']] <-
     "LOSS_OF_FUNCTION",
     "GENENAME",
     "PROTEIN_DOMAIN",
+    "DP_CONTROL",
     "GWAS_CITATION",
     "HGVSp",
     "HGVSc",
@@ -114,6 +117,7 @@ col_format_output[['tsv']] <-
     "VAR_ID",
     "GENOME_VERSION",
     "GENOTYPE",
+    "DP_CONTROL",
     "CPSR_CLASSIFICATION_SOURCE",
     "VARIANT_CLASS",
     "CODING_STATUS",
@@ -178,6 +182,7 @@ col_format_output[['html_bm']] <-
     'CONSEQUENCE',
     'BM_EVIDENCE_LEVEL',
     'GENOTYPE',
+    "DP_CONTROL",
     'BM_CANCER_TYPE',
     'BM_DISEASE_ONTOLOGY_ID',
     'BM_PRIMARY_SITE',
@@ -212,6 +217,7 @@ col_format_output[['xlsx_classification']] <-
   c("SAMPLE_ID",
     "GENOMIC_CHANGE",
     "GENOTYPE",
+    "DP_CONTROL",
     "GENOME_VERSION",
     "VARIANT_CLASS",
     "SYMBOL",
@@ -253,6 +259,7 @@ col_format_output[['xlsx_secondary']] <-
   c("SAMPLE_ID",
     "GENOMIC_CHANGE",
     "GENOTYPE",
+    "DP_CONTROL",
     "GENOME_VERSION",
     "VARIANT_CLASS",
     "SYMBOL",
@@ -292,6 +299,7 @@ col_format_output[['xlsx_biomarker']] <-
   c("SAMPLE_ID",
     "GENOMIC_CHANGE",
     "GENOTYPE",
+    "DP_CONTROL",
     "GENOME_VERSION",
     "VARIANT_CLASS",
     "SYMBOL",

inst/templates/quarto/cpsr_biomarkers.qmd

@@ -40,14 +40,16 @@ for (etype in c("Predictive","Diagnostic","Predisposing","Prognostic")) {
 
 - Germline DNA variants (__class 4/5__) in the targeted cancer predisposition genes that match with reported clinical evidence items from [CIViC](https://civicdb.org) and [CGI biomarker database](https://www.cancergenomeinterpreter.org/biomarkers) are listed. 
 
-- Total number of _variant-clinical evidence associations_ that have been detected:
-    * Predisposing: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_predisposing`__
-    * Predictive: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_predictive`__ 
-    * Prognostic: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_prognostic`__ 
-    * Diagnostic: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_diagnostic`__
+- Total number of _unique variants_ with clinical evidence associations: __N = `r cps_report[['content']][['snv_indel']]$v_stat_bm$n_var_eitems`__
+
+- Total number of detected _variant-clinical evidence associations_:
+    * Predictive: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_eitems_predictive`__ 
+    * Predisposing: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_eitems_predisposing`__
+    * Prognostic: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_eitems_prognostic`__ 
+    * Diagnostic: __`r cps_report[['content']][['snv_indel']]$v_stat_bm$n_eitems_diagnostic`__
 
 ::: {.callout-note}
-The same genetic variant may match with multiple evidence items, pending on the e.g. _disease context_, _therapeutic context_, _biomarker resolution_, or underlying _evidence source_ (publication)
+As indicated from the variant-association numbers above, the same germline mutation may potentially match with multiple evidence items, pending on e.g. the _disease context_, _therapeutic context_, _biomarker resolution_, or underlying _evidence source_ (i.e. publication)
 :::
 
 ```{r biomarker_note}

inst/templates/quarto/cpsr_classification.qmd

@@ -69,8 +69,8 @@ formula_gnomad <- as.formula(paste0("~", rlang::sym(tag_gnomad)))
 
 <br>
 
-   *  A total of n = __`r tot_variants[['class5']][['ClinVar']]`__ variants are registered with a <i>Pathogenic</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
-   *  A total of n = __`r tot_variants[['class5']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Pathogenic</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
+   *  A total of __N = `r tot_variants[['class5']][['ClinVar']]`__ variants are registered with a <i>Pathogenic</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
+   *  A total of __N = `r tot_variants[['class5']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Pathogenic</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
 
 ::: {.callout-note}
 Variants displayed here constitute the top 2000 variants for each of the ClinVar and non-ClinVar variant sets (due to display limitations with client-side tables)
@@ -126,6 +126,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class5_1, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class5_1, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class5_1, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class5_1, ~SYMBOL)
   ),
   list(
@@ -206,6 +210,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class5_2, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class5_2, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class5_2, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class5_2, ~SYMBOL)
   ),
   list(
@@ -247,8 +255,8 @@ htmltools::br()
 
 <br>
 
-*  A total of n = __`r tot_variants[['class4']][['ClinVar']]`__ variants are recorded with a <i>Likely Pathogenic</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
-*  A total of n = __`r tot_variants[['class4']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Likely Pathogenic</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
+*  A total of __N = `r tot_variants[['class4']][['ClinVar']]`__ variants are recorded with a <i>Likely Pathogenic</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
+*  A total of __N = `r tot_variants[['class4']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Likely Pathogenic</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
 
 ::: {.callout-note}
 Variants displayed here constitute the top 2000 variants for each of the ClinVar and non-ClinVar variant sets (due to display limitations with client-side tables)
@@ -303,6 +311,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class4_1, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class4_1, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class4_1, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class4_1, ~SYMBOL)
   ),
   list(
@@ -384,6 +396,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class4_2, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class4_2, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class4_2, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class4_2, ~SYMBOL)
   ),
   list(
@@ -424,8 +440,8 @@ htmltools::br()
 
 <br>
 
-*  A total of n = __`r tot_variants[['class3']][['ClinVar']]`__ variants are recorded with a <i>VUS</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
-*  A total of n = __`r tot_variants[['class3']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>VUS</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
+*  A total of __N = `r tot_variants[['class3']][['ClinVar']]`__ variants are recorded with a <i>VUS</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
+*  A total of __N = `r tot_variants[['class3']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>VUS</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
 
 ::: {.callout-note}
 Variants displayed here constitute the top 2000 variants for each of the ClinVar and non-ClinVar variant sets (due to display limitations with client-side tables)
@@ -478,6 +494,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class3_1, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class3_1, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class3_1, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class3_1, ~SYMBOL),
     crosstalk::filter_slider("GERP_SCORE", "Genomic conservation score (GERP)", 
                              variants_class3_1, ~GERP_SCORE,
@@ -580,6 +600,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class3_2, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class3_2, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class3_2, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class3_2, ~SYMBOL),
     crosstalk::filter_slider("GERP_SCORE", "Genomic conservation score (GERP)", variants_class3_2, ~GERP_SCORE,
       min = -12.3, max = 6.17, ticks = T
@@ -634,8 +658,8 @@ htmltools::br()
 
 <br>
 
-*  A total of n = __`r tot_variants[['class2']][['ClinVar']]`__ variants are recorded with a <i>Likely Benign</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
-*  A total of n = __`r tot_variants[['class2']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Likely Benign</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
+*  A total of __N = `r tot_variants[['class2']][['ClinVar']]`__ variants are recorded with a <i>Likely Benign</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
+*  A total of __N = `r tot_variants[['class2']][['CPSR_ACMG']]`__ <i><b>non-ClinVar</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Likely Benign</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
 
 ::: {.callout-note}
 Variants displayed here constitute the top 2000 variants for each of the ClinVar and non-ClinVar variant sets (due to display limitations with client-side tables)
@@ -691,6 +715,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class2_1, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class2_1, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class2_1, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class2_1, ~SYMBOL)
   ),
   list(
@@ -773,6 +801,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class2_2, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class2_2, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class2_2, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class2_2, ~SYMBOL)
   ),
   list(
@@ -812,8 +844,8 @@ htmltools::br()
 
 <br>
 
-*  A total of n = __`r tot_variants[['class1']][['ClinVar']]`__ variants are recorded with a <i>Benign</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
-*  A total of n = __`r tot_variants[['class1']][['CPSR_ACMG']]`__ <i><b>Other</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Benign</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
+*  A total of __N = `r tot_variants[['class1']][['ClinVar']]`__ variants are recorded with a <i>Benign</i> clinical significance in the [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) database.
+*  A total of __N = `r tot_variants[['class1']][['CPSR_ACMG']]`__ <i><b>Other</b></i> variants (i.e. not submitted to/recorded in ClinVar) are classified with a <i>Benign</i> clinical significance by CPSR (refined ACMG criteria - based on population frequency and variant effect).
 
 ::: {.callout-note}
 Variants displayed here constitute the top 2000 variants for each of the ClinVar and non-ClinVar variant sets (due to display limitations with client-side tables)
@@ -867,6 +899,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class1_1, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class1_1, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class1_1, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class1_1, ~SYMBOL)
   ),
   list(
@@ -950,6 +986,10 @@ crosstalk::bscols(
   list(
     crosstalk::filter_select("CONSEQUENCE", "Consequence", variants_class1_2, ~CONSEQUENCE),
     crosstalk::filter_checkbox("GENOTYPE", "Genotype", variants_class1_2, ~GENOTYPE),
+    if(cps_report$settings$conf$sample_properties$dp_detected == 1){
+      crosstalk::filter_slider("DP_CONTROL", "Variant sequencing depth", 
+                             variants_class1_2, ~DP_CONTROL)
+    },
     crosstalk::filter_select("SYMBOL", "Gene", variants_class1_2, ~SYMBOL)
   ),
   list(

inst/templates/quarto/cpsr_secondary_findings.qmd

@@ -12,7 +12,7 @@ acmg_version <- cps_report$settings$reference_data$source_metadata[
 acmg_url <- cps_report$settings$reference_data$source_metadata[
   cps_report$settings$reference_data$source_metadata$source_abbreviation == "acmg_sf","source_url"]
 genotypes_unavailable <- !(as.logical(
-  cps_report$settings$conf$sample_properties$genotypes_available))
+  cps_report$settings$conf$sample_properties$gt_detected))
 
 ```
 
@@ -26,7 +26,7 @@ cat("::: {.callout-warning}\n\n**Secondary findings not assessed due to lacking
 ```
 
 
-*  For the sample in question, a total of n = __`r tot_sf_variants`__ variants in [genes recommended for secondary findings reporting (ACMG `r acmg_version`)](`r acmg_url`) 
+*  For the sample in question, a total of __N = `r tot_sf_variants`__ variants in [genes recommended for secondary findings reporting (ACMG `r acmg_version`)](`r acmg_url`) 
 are registered with a <i>Pathogenic/Likely pathogenic</i> clinical significance in ClinVar.
 
 <br>

inst/templates/quarto/cpsr_summary.qmd

@@ -89,7 +89,7 @@ bslib::layout_column_wrap(
     showcase_layout = "left center"
   ),
   bslib::value_box(
-    title = "Cancer predisposition genes affected",
+    title = "Genes affected by pathogenic variants",
     value = genes_value_box,
     showcase = bsicons::bs_icon("bullseye"),
     theme = bslib::value_box_theme(